Open xapple opened 1 year ago
I installed PanGIA by cloning this repository and then downloading these two files:
$ curl -O https://edge-dl.lanl.gov/PanGIA/database/PanGIA_20190830_taxonomy.tar.gz $ curl -O https://edge-dl.lanl.gov/PanGIA/database/PanGIA_20190830_NCBI_genomes_refseq89_BAV.fa.mmi.tar.gz $ tar xzf PanGIA_20190830_taxonomy.tar.gz $ tar xzf PanGIA_20190830_NCBI_genomes_refseq89_BAV.fa.mmi.tar.gz
Next, I ran the following command to test if PanGIA could classify a bunch of artificially generated reads:
(pangia) xapple@server ~ $ ~/programs/pangia/bin/pangia.py --threads 4 --database ~/databases/pangia/PanGIA/NCBI_genomes_refseq89_BAV.fa --mode report --outdir ~/runs/pangia_test/ --readmapper minimap2 --prefix sample --input ~/runs/pangia_test/reads_fwd.fastq.gz ~/runs/pangia_test/reads_rev.fastq.gz
But it throws a KeyError and seems to be non-functional.
KeyError
[00:00:00] Starting PanGIA 1.0.0-RC6.1 [00:00:00] Temporary directory '~/runs/pangia_test//sample_tmp' found. Deleting directory... [00:04:53] Arguments and dependencies checked: [00:04:53] Input reads : ['~/runs/pangia_test/reads_fwd.fastq.gz', '~/runs/pangia_test/reads_rev.fastq.gz'] [00:04:53] Input SAM file : ~/runs/pangia_test//sample.pangia.sam [00:04:53] Input background : None [00:04:53] Save background : None [00:04:53] Scoring method : standalone [00:04:53] Scoring parameter : 0.5:0.99 [00:04:53] Database : ['~/databases/pangia/PanGIA/NCBI_genomes_refseq89_BAV.fa.mmi'] [00:04:53] Abundance : DEPTH_COV [00:04:53] Output path : ~/runs/pangia_test/ [00:04:53] Prefix : sample [00:04:53] Mode : report [00:04:53] Specific taxid : None [00:04:53] Threads : 4 [00:04:53] First #refs in XA : 30 [00:04:53] Extra NM in XA : 1 [00:04:53] Minimal score : 0 [00:04:53] Minimal RSNB : 2.5 [00:04:53] Minimal reads : 10 [00:04:53] Minimal linear len: 200 [00:04:53] Minimal genome cov: 0.004 [00:04:53] Minimal depth (DC): 0.01 [00:04:53] Minimal RSDCnr : 0.0009 [00:04:53] Aligner option : -A1 -B2 -k 40 -m 60 -x sr -p 1 -N 30 [00:04:53] Aligner seed len : 40 [00:04:53] Aligner min score : 60 [00:04:53] Aligner path : ~/mambaforge/envs/pangia/bin/minimap2 [00:04:53] Samtools path : ~/mambaforge/envs/pangia/bin/samtools [00:04:53] Loading taxonomy information... [00:05:00] Done. [00:05:00] Loading pathogen information... [00:05:00] Done. 2817 pathogens loaded. [00:05:00] Loading taxonomic uniqueness information... [00:05:00] Done. 31177 taxonomic uniqueness loaded. [00:05:00] Loading sizes of genomes... [00:05:55] Done. 1061 target and 0 host genome(s) loaded. [00:05:55] Running read-mapping... [00:05:55] Mapping to ~/databases/pangia/PanGIA/NCBI_genomes_refseq89_BAV.fa.mmi... [00:06:53] Done mapping reads to the database(s). [00:06:53] Merging SAM files... [00:06:55] Logfile saved to ~/runs/pangia_test//sample.pangia.log. [00:06:55] Done. Mapped SAM file saved to ~/runs/pangia_test//sample.pangia.sam. [00:06:55] Total number of input reads: 400013 [00:06:55] Total number of mapped reads: 186478 [00:06:55] Total number of host reads: 0 (0.00%) [00:06:55] Total number of ignored reads (cross superkingdom): 349 (0.19%) [00:06:55] Processing SAM file... [00:06:55] Parsing SAM files with 4 subprocesses... [00:06:59] Merging results... [00:06:59] Done. [00:06:59] Calculating linear length... [00:07:02] Done processing SAM file, 184670 alignment(s). [00:07:02] Rolling up taxonomies... [00:07:02] 17 strain(s) mapped. Traceback (most recent call last): File "~/programs/pangia/bin/pangia.py", line 2320, in <module> res_rollup = taxonomyRollUp(res, patho_meta, mapped_r_cnt, argvs.minRsnb, argvs.minReads, argvs.minLen, argvs.minCov, argvs.minDc) File "~/programs/pangia/bin/pangia.py", line 1199, in taxonomyRollUp genome_size[taxid] KeyError: '1582156.1'
I installed PanGIA by cloning this repository and then downloading these two files:
Next, I ran the following command to test if PanGIA could classify a bunch of artificially generated reads:
But it throws a
KeyErrorand seems to be non-functional.